[gmx-users] Re: simulating with air

[Vitaly Chaban]

There is no need to use x2top to make so primitive topology. It is
much easier to type it by hand. But even if you decided to do it you
should firstly add the 1-bonded nitrogen (and I guess, the same for
oxygen further) atom to ffgmx.n2t file.

If I were you I would make the own FF not to depend on any standard one.

[atomtype]
N ................
O ................
C ................

[molecule]
................

[atoms]
N .................
N ................

[bondtypes]
......................


And so on.
Also don't forget to point out LJ parameters, not only bond constants.


2008/8/14 Andy Shelley <robert.shelley at gmail.com>:
> I am currently just trying to get 1 molecule to work.
> So I added the morse potential to ffgmxbon.itp as:
>
> [ bondtypes ]
>   ; i    j func        b0          kb
>     N    N    3   0.10980     943.0433    0.2642
>
> and received this error message after using x2top with an ENCAD force field
>
> Fatal error: No forcefield type for atom N (1) with 1 bonds
>
> Any ideas on what might be causing the error. I am also using GROMACS 3.3.1.
>
> Thanks,
> Andy
>
>



-- 
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq., 4, Kharkiv 61077, Ukraine
email: chaban at univer.kharkov.ua
skype: vvchaban